H.R.933, the 2013 Consolidated and Further Continuing Appropriations Act, authorized HUD to raise the fee to up to 3 percent. A notice that was published in today's issue of the Federal Register sets the fee at 1.5 percent, up from the current 1 percent.

The fee, which is based on the total loan amount, is passed on to the borrower. Typically, it's added to the mortgage for the Native buyer who participates in the Section 184 program but it also can be paid in cash.

'The Section 184 program charges borrowers a guarantee fee to participate in the program and the fee, along with other funds and appropriations, is used to fulfill obligations of the Secretary with respect to the loans guaranteed under this section," a second notice states.

HUD set the new fee without putting it to public comment and without consulting tribes, according to the second notice.

As of 2010, Section 184 has guaranteed over 12,000 loans, totaling nearly $2 billion, according to HUD.